private void StandardsChanged(object sender, EventArgs eventArgs)
{
if (!FireStandardsChanged)
{
return;
}
var oldPeps = comboMinPeptide.Items.Cast <string>().ToArray();
var newPeps = StandardPeptideList.Select(pep => pep.Sequence).ToArray();
if (oldPeps.SequenceEqual(newPeps))
{
return;
}
UpdatePeptideCount();
var curMin = (string)comboMinPeptide.SelectedItem;
var curMax = (string)comboMaxPeptide.SelectedItem;
comboMinPeptide.Items.Clear();
comboMaxPeptide.Items.Clear();
if (newPeps.Length == 0 || !comboMinPeptide.Enabled)
{
return;
}
comboMinPeptide.Items.AddRange(newPeps);
comboMaxPeptide.Items.AddRange(newPeps);
var newMinIdx = newPeps.IndexOf(pep => pep.Equals(curMin));
if (newMinIdx < 0)
{
newMinIdx = 0;
}
var newMaxIdx = newPeps.IndexOf(pep => pep.Equals(curMax));
if (newMaxIdx < 0)
{
newMaxIdx = comboMaxPeptide.Items.Count - 1;
}
if (newMinIdx > newMaxIdx)
{
var tmp = newMinIdx;
newMinIdx = newMaxIdx;
newMaxIdx = tmp;
}
comboMinPeptide.SelectedIndex = newMinIdx;
comboMaxPeptide.SelectedIndex = newMaxIdx;
}
private void UpdateEquation(object sender, EventArgs e)
{
if (!TryGetLine(false, out var line))
{
lblEquation.Text = string.Empty;
if (!IsRecalibration)
{
FireStandardsChanged = false;
StandardPeptideList.ForEach(pep => pep.Irt = double.NaN);
StandardPeptideList.ResetBindings();
FireStandardsChanged = true;
}
return;
}
var equationSb = new StringBuilder();
equationSb.Append(Resources.CalibrateIrtDlg_UpdateControls_iRT);
equationSb.Append(@" =");
var roundedSlope = Math.Round(line.Slope, 4);
var roundedIntercept = Math.Round(line.Intercept, 4);
if (roundedSlope != 0 || roundedIntercept != 0)
{
if (roundedSlope != 0)
{
if (roundedSlope != 1)
{
equationSb.Append(string.Format(@" {0:F04} *", roundedSlope));
}
equationSb.Append(' ');
equationSb.Append(Resources.CalibrateIrtDlg_UpdateControls_RT);
}
if (roundedIntercept != 0)
{
equationSb.Append(roundedSlope != 0
? string.Format(@" {0} {1:F04}", roundedIntercept >= 0 ? '+' : '-', Math.Abs(roundedIntercept))
: string.Format(@" {0:F04}", roundedIntercept));
}
}
else
{
equationSb.Append(string.Format(@" {0:F04}", 0));
}
lblEquation.Text = equationSb.ToString();
if (!IsRecalibration && !SelectedRegressionOption.ForcedIrts)
{
FireStandardsChanged = false;
StandardPeptideList.ForEach(pep => pep.Irt = line.GetY(pep.RetentionTime));
StandardPeptideList.ResetBindings();
FireStandardsChanged = true;
}
}
public void StandardsChanged(object sender, EventArgs eventArgs)
{
var oldPeps = comboMinPeptide.Items.Cast <string>().ToArray();
var newPeps = StandardPeptideList.Select(pep => pep.Sequence).ToArray();
if (oldPeps.SequenceEqual(newPeps))
{
return;
}
labelStandardCount.Text = StandardPeptideList.Count != 1
? ModeUIAwareStringFormat(Resources.CalibrateIrtDlg_StandardsChanged__0__peptides, StandardPeptideCount)
: ModeUIAwareStringFormat(Resources.CalibrateIrtDlg_StandardsChanged__1_peptide);
var curMin = (string)comboMinPeptide.SelectedItem;
var curMax = (string)comboMaxPeptide.SelectedItem;
comboMinPeptide.Items.Clear();
comboMaxPeptide.Items.Clear();
if (newPeps.Length == 0 || !comboMinPeptide.Enabled)
{
return;
}
comboMinPeptide.Items.AddRange(newPeps);
comboMaxPeptide.Items.AddRange(newPeps);
var newMinIdx = newPeps.IndexOf(pep => pep.Equals(curMin));
if (newMinIdx < 0)
{
newMinIdx = 0;
}
var newMaxIdx = newPeps.IndexOf(pep => pep.Equals(curMax));
if (newMaxIdx < 0)
{
newMaxIdx = comboMaxPeptide.Items.Count - 1;
}
if (newMinIdx > newMaxIdx)
{
var tmp = newMinIdx;
newMinIdx = newMaxIdx;
newMaxIdx = tmp;
}
comboMinPeptide.SelectedIndex = newMinIdx;
comboMaxPeptide.SelectedIndex = newMaxIdx;
}
private void comboRegression_SelectedIndexChanged(object sender, EventArgs e)
{
labelMinIrt.Enabled = textMinIrt.Enabled = labelMaxIrt.Enabled = textMaxIrt.Enabled =
labelMinPeptide.Enabled = comboMinPeptide.Enabled = labelMaxPeptide.Enabled = comboMaxPeptide.Enabled = SelectedRegressionOption.AllowEditEquation;
if (!SelectedRegressionOption.AllowEditEquation)
{
textMinIrt.Clear();
textMaxIrt.Clear();
comboMinPeptide.Items.Clear();
comboMaxPeptide.Items.Clear();
}
lblEquation.Visible = calibrateMeasuredRt.Visible = !SelectedRegressionOption.ForcedIrts;
if (IsRecalibration)
{
UpdateEquation(sender, e);
return;
}
calibratePeptides.ReadOnly = calibrateMeasuredRt.ReadOnly = !SelectedRegressionOption.AllowEditGrid;
gridViewCalibrate.AllowUserToAddRows = gridViewCalibrate.AllowUserToDeleteRows = SelectedRegressionOption.AllowEditGrid;
if (SelectedRegressionOption.ForcedStandards)
{
_gridViewDriver.SetPeptides(SelectedRegressionOption.StandardPeptides.Select(pep => new StandardPeptide(pep)).ToArray());
return;
}
if (SelectedRegressionOption.MatchedPeptideCount == 0) // fixed point
{
StandardsChanged(sender, e);
UpdateEquation(sender, e);
return;
}
// If standard peptide list is empty, or contains over 50% of the selected regression's peptides, use results
var regressionPeptides = new TargetMap <bool>(SelectedRegressionOption.MatchedRegressionPeptides.Select(match =>
new KeyValuePair <Target, bool>(match.Item1.ModifiedTarget, true)));
if (StandardPeptideCount == 0 || StandardPeptideList.Count(pep => regressionPeptides.ContainsKey(pep.Target)) >= regressionPeptides.Count / 2)
{
if (!SetCalibrationPeptides())
{
comboRegression.SelectedIndex = 0;
return;
}
}
UpdateEquation(sender, e);
}
public void SetFixedPoints(int one, int two)
{
int count = StandardPeptideList.Count;
if (one >= two || two >= count)
{
return;
}
for (int i = 0; i < count; i++)
{
bool fixedPoint = (i == one || i == two);
var peptide = StandardPeptideList[i];
if (peptide.FixedPoint != fixedPoint)
{
peptide.FixedPoint = fixedPoint;
StandardPeptideList.ResetItem(i);
}
}
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
if (!helper.ValidateNameTextBox(textName, out var name))
{
return;
}
else if (_existing.Contains(r => !ReferenceEquals(_standard, r) && Equals(name, r.Name)))
{
helper.ShowTextBoxError(textName, Resources.CalibrateIrtDlg_OkDialog_The_iRT_standard__0__already_exists_, name);
return;
}
if (!TryGetLine(true, out var linearEquation))
{
return;
}
if (!IsRecalibration)
{
IrtStandard = new IrtStandard(name, null,
StandardPeptideList.Select(pep => new DbIrtPeptide(pep.Target, pep.Irt, true, TimeSource.peak)));
}
else
{
foreach (var pep in _updatePeptides)
{
pep.Irt = linearEquation.GetY(pep.Irt);
}
IrtStandard = new IrtStandard(name, null,
_standard.Peptides.Select(pep =>
new DbIrtPeptide(pep.Target, linearEquation.GetY(pep.Irt), true, TimeSource.peak)));
}
DialogResult = DialogResult.OK;
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
if (!helper.ValidateNameTextBox(textName, out var name))
{
return;
}
else if (_existing.Contains(r => !ReferenceEquals(_standard, r) && Equals(name, r.Name)))
{
helper.ShowTextBoxError(textName, Resources.CalibrateIrtDlg_OkDialog_The_iRT_standard__0__already_exists_, name);
return;
}
if (!IsRecalibration)
{
var irts = IrtStandard.CIRT.Peptides.ToDictionary(p => p.GetNormalizedModifiedSequence(), p => p.Irt);
var calibrationPeptides = new List <Tuple <DbIrtPeptide, double> >();
foreach (var pep in StandardPeptideList)
{
double irt;
if (!irts.TryGetValue(SequenceMassCalc.NormalizeModifiedSequence(pep.Target), out irt))
{
break;
}
calibrationPeptides.Add(new Tuple <DbIrtPeptide, double>(
new DbIrtPeptide(pep.Target, irt, true, TimeSource.peak), pep.RetentionTime));
}
if (calibrationPeptides.Count == StandardPeptideList.Count)
{
var statStandard = new Statistics(calibrationPeptides.Select(p => p.Item1.Irt));
var statMeasured = new Statistics(calibrationPeptides.Select(p => p.Item2));
if (statStandard.R(statMeasured) >= RCalcIrt.MIN_IRT_TO_TIME_CORRELATION)
{
var result = MultiButtonMsgDlg.Show(this,
Resources.CalibrateIrtDlg_OkDialog_All_of_these_peptides_are_known_CiRT_peptides__Would_you_like_to_use_the_predefined_iRT_values_,
MultiButtonMsgDlg.BUTTON_YES, MultiButtonMsgDlg.BUTTON_NO, true);
if (result == DialogResult.Cancel)
{
return;
}
if (result == DialogResult.Yes)
{
IrtStandard = new IrtStandard(name, null, calibrationPeptides.Select(x => x.Item1));
DialogResult = DialogResult.OK;
return;
}
}
}
}
if (!TryGetLine(true, out var linearEquation))
{
return;
}
if (!IsRecalibration)
{
IrtStandard = new IrtStandard(name, null,
StandardPeptideList.Select(pep =>
new DbIrtPeptide(pep.Target, linearEquation.GetY(pep.RetentionTime), true, TimeSource.peak)));
}
else
{
foreach (var pep in _updatePeptides)
{
pep.Irt = linearEquation.GetY(pep.Irt);
}
IrtStandard = new IrtStandard(name, null,
_standard.Peptides.Select(pep =>
new DbIrtPeptide(pep.Target, linearEquation.GetY(pep.Irt), true, TimeSource.peak)));
}
DialogResult = DialogResult.OK;
}
